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Gurkenkönig
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10
@gurkenkonig-16328
Last seen 5.2 years ago
The method produces different results with each run. Can anyone give me a hint on how to fix this behavior?
set.seed(42)
library("ChAMP")
myLoad_test1 <- champ.load(directory = "data/raw/iDat_t0",
method="ChAMP",
methValue="B",
autoimpute=TRUE,
filterDetP=TRUE,
ProbeCutoff=0,
SampleCutoff=0.1,
detPcut=0.01,
filterBeads=TRUE,
beadCutoff=0.05,
filterNoCG=TRUE,
filterSNPs=TRUE,
population=NULL,
filterMultiHit=TRUE,
filterXY=TRUE,
force=FALSE,
arraytype="EPIC")
gc()
myNorm_test_1.1 <- champ.norm(beta=myLoad_test1$beta,
rgSet=myLoad_test1$rgSet,
mset=myLoad_test1$mset,
resultsDir="./CHAMP_Normalization/",
method="BMIQ",
plotBMIQ=FALSE,
arraytype="EPIC",
cores=1)
gc()
myNorm_test_1.2 <- champ.norm(beta=myLoad_test1$beta,
rgSet=myLoad_test1$rgSet,
mset=myLoad_test1$mset,
resultsDir="./CHAMP_Normalization/",
method="BMIQ",
plotBMIQ=FALSE,
arraytype="EPIC",
cores=1)
print(identical(myNorm_test_1.1, myNorm_test_1.2))
myNorm_test_1.1[1:5,1:5]
myNorm_test_1.2[1:5,1:5]
[1] FALSE
SPL-066 SPL-005 SPL-001 SPL-013 SPL-021
cg07881041 0.96269795 0.93971660 0.96005661 0.96662973 0.94678340
cg03513874 0.96182761 0.96468813 0.96690889 0.96146023 0.95427445
cg05451842 0.02726911 0.03012527 0.03381639 0.02627537 0.02072133
cg14797042 0.97285162 0.98219496 0.97348613 0.96923460 0.98554301
cg09838562 0.02913757 0.02983066 0.03453992 0.04064944 0.02684536
SPL-066 SPL-005 SPL-001 SPL-013 SPL-021
cg07881041 0.96152149 0.94004936 0.96097521 0.96574810 0.94501442
cg03513874 0.96063812 0.96527364 0.96765142 0.96053807 0.95271938
cg05451842 0.02757454 0.02976092 0.03170889 0.03010782 0.01929390
cg14797042 0.97184842 0.98277645 0.97406201 0.96837768 0.98495060
cg09838562 0.02944406 0.02948598 0.03235829 0.05618163 0.02507286
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChAMP_2.12.4 IlluminaHumanMethylationEPICmanifest_0.3.0
[3] Illumina450ProbeVariants.db_1.18.0 DMRcate_1.18.0
[5] DMRcatedata_1.18.0 DSS_2.30.1
[7] bsseq_1.18.0 FEM_3.10.0
[9] graph_1.60.0 org.Hs.eg.db_3.7.0
[11] impute_1.56.0 igraph_1.2.4
[13] corrplot_0.84 marray_1.60.0
[15] limma_3.38.3 Matrix_1.2-14
[17] AnnotationDbi_1.44.0 ChAMPdata_2.14.1
[19] minfi_1.28.3 bumphunter_1.24.5
[21] locfit_1.5-9.1 iterators_1.0.10
[23] foreach_1.4.4 Biostrings_2.50.2
[25] XVector_0.22.0 SummarizedExperiment_1.12.0
[27] DelayedArray_0.8.0 BiocParallel_1.16.6
[29] matrixStats_0.54.0 Biobase_2.42.0
[31] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[33] IRanges_2.16.0 S4Vectors_0.20.1
[35] BiocGenerics_0.28.0 RevoUtils_11.0.1
[37] RevoUtilsMath_11.0.0
loaded via a namespace (and not attached):
[1] rtracklayer_1.42.1 prabclus_2.2-7
[3] R.methodsS3_1.7.1 wateRmelon_1.26.0
[5] pkgmaker_0.27 tidyr_0.8.2
[7] ggplot2_3.1.0 acepack_1.4.1
[9] bit64_0.9-7 knitr_1.21
[11] R.utils_2.8.0 data.table_1.12.0
[13] rpart_4.1-13 RCurl_1.95-4.11
[15] GEOquery_2.50.5 AnnotationFilter_1.6.0
[17] doParallel_1.0.14 GenomicFeatures_1.34.3
[19] preprocessCore_1.44.0 RSQLite_2.1.1
[21] combinat_0.0-8 bit_1.1-14
[23] xml2_1.2.0 httpuv_1.4.5.1
[25] assertthat_0.2.0 IlluminaHumanMethylation450kmanifest_0.4.0
[27] viridis_0.5.1 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[29] isva_1.9 xfun_0.5
[31] hms_0.4.2 evaluate_0.13
[33] missMethyl_1.16.0 DNAcopy_1.56.0
[35] promises_1.0.1 DEoptimR_1.0-8
[37] progress_1.2.0 dendextend_1.9.0
[39] DBI_1.0.0 htmlwidgets_1.3
[41] reshape_0.8.8 purrr_0.3.0
[43] ROC_1.58.0 dplyr_0.7.6
[45] backports_1.1.3 trimcluster_0.1-2.1
[47] permute_0.9-4 annotate_1.60.0
[49] biomaRt_2.38.0 ensembldb_2.6.6
[51] withr_2.1.2 globaltest_5.36.0
[53] Gviz_1.26.5 robustbase_0.93-3
[55] BSgenome_1.50.0 checkmate_1.9.1
[57] GenomicAlignments_1.18.1 prettyunits_1.0.2
[59] mclust_5.4.2 cluster_2.0.7-1
[61] RPMM_1.25 lazyeval_0.2.1
[63] crayon_1.3.4 genefilter_1.64.0
[65] pkgconfig_2.0.2 nlme_3.1-137
[67] ProtGenerics_1.14.0 nnet_7.3-12
[69] bindr_0.1.1 rlang_0.3.1
[71] diptest_0.75-7 nleqslv_3.3.2
[73] registry_0.5 affyio_1.52.0
[75] dichromat_2.0-0 rngtools_1.3.1
[77] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 base64_2.0
[79] Rhdf5lib_1.4.2 base64enc_0.1-3
[81] geneLenDataBase_1.18.0 whisker_0.3-2
[83] viridisLite_0.3.0 bitops_1.0-6
[85] R.oo_1.22.0 KernSmooth_2.23-15
[87] blob_1.1.1 DelayedMatrixStats_1.4.0
[89] doRNG_1.7.1 stringr_1.4.0
[91] qvalue_2.14.1 nor1mix_1.2-3
[93] readr_1.3.1 scales_1.0.0
[95] memoise_1.1.0 magrittr_1.5
[97] plyr_1.8.4 bibtex_0.4.2
[99] zlibbioc_1.28.0 compiler_3.5.1
[101] RColorBrewer_1.1-2 illuminaio_0.24.0
[103] clue_0.3-56 Rsamtools_1.34.1
[105] affy_1.60.0 JADE_2.0-1
[107] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 htmlTable_1.13.1
[109] Formula_1.2-3 MASS_7.3-50
[111] mgcv_1.8-24 tidyselect_0.2.5
[113] stringi_1.1.7 yaml_2.2.0
[115] askpass_1.1 latticeExtra_0.6-28
[117] grid_3.5.1 VariantAnnotation_1.28.11
[119] tools_3.5.1 ruv_0.9.7
[121] rstudioapi_0.9.0 foreign_0.8-70
[123] gridExtra_2.3 digest_0.6.18
[125] BiocManager_1.30.4 shiny_1.2.0
[127] quadprog_1.5-5 fpc_2.1-11.1
[129] bindrcpp_0.2.2 Rcpp_1.0.0
[131] siggenes_1.56.0 later_0.8.0
[133] httr_1.4.0 biovizBase_1.30.1
[135] lumi_2.34.0 kernlab_0.9-27
[137] colorspace_1.4-0 XML_3.98-1.17
[139] statmod_1.4.30 kpmt_0.1.0
[141] multtest_2.38.0 shinythemes_1.1.2
[143] flexmix_2.3-15 plotly_4.8.0
[145] xtable_1.8-3 jsonlite_1.6
[147] modeltools_0.2-22 R6_2.4.0
[149] Hmisc_4.2-0 pillar_1.3.1
[151] htmltools_0.3.6 mime_0.6
[153] glue_1.3.0 class_7.3-14
[155] beanplot_1.2 codetools_0.2-16
[157] mvtnorm_1.0-8 lattice_0.20-35
[159] tibble_2.0.1 sva_3.30.1
[161] curl_3.3 BiasedUrn_1.07
[163] gtools_3.8.1 GO.db_3.7.0
[165] openssl_1.2.1 survival_2.42-3
[167] rmarkdown_1.11 methylumi_2.28.0
[169] fastICA_1.2-1 munsell_0.5.0
[171] rhdf5_2.26.2 GenomeInfoDbData_1.2.0
[173] goseq_1.34.1 HDF5Array_1.10.1
[175] reshape2_1.4.3 gtable_0.2.0
